3I7B

Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with bumped kinase inhibitor NM-PP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors.

Ojo, K.K.Larson, E.T.Keyloun, K.R.Castaneda, L.J.Derocher, A.E.Inampudi, K.K.Kim, J.E.Arakaki, T.L.Murphy, R.C.Zhang, L.Napuli, A.J.Maly, D.J.Verlinde, C.L.Buckner, F.S.Parsons, M.Hol, W.G.Merritt, E.A.Van Voorhis, W.C.

(2010) Nat Struct Mol Biol 17: 602-607

  • DOI: 10.1038/nsmb.1818
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • New drugs are needed to treat toxoplasmosis. Toxoplasma gondii calcium-dependent protein kinases (TgCDPKs) are attractive targets because they are absent in mammals. We show that TgCDPK1 is inhibited by low nanomolar levels of bumped kinase inhibitor ...

    New drugs are needed to treat toxoplasmosis. Toxoplasma gondii calcium-dependent protein kinases (TgCDPKs) are attractive targets because they are absent in mammals. We show that TgCDPK1 is inhibited by low nanomolar levels of bumped kinase inhibitors (BKIs), compounds inactive against mammalian kinases. Cocrystal structures of TgCDPK1 with BKIs confirm that the structural basis for selectivity is due to the unique glycine gatekeeper residue in the ATP-binding site. We show that BKIs interfere with an early step in T. gondii infection of human cells in culture. Furthermore, we show that TgCDPK1 is the in vivo target of BKIs because T. gondii expressing a glycine to methionine gatekeeper mutant enzyme show significantly decreased sensitivity to BKIs. Thus, design of selective TgCDPK1 inhibitors with low host toxicity may be achievable.


    Related Citations: 
    • Discovery of Potent and Selective Inhibitors of CDPK1 from C. parvum and T. gondii
      Murphy, R.C., Ojo, K.K., Larson, E.T., Castellanos-Gonzalez, A., Perera, B.G.K., Keyloun, K.R., Kim, J.E., Bhandari, J.G., Muller, N.R., Verlinde, C.L.M.J., White Jr, A.C., Merritt, E.A., Van Voorhis, W.C., Maly, D.J.
      (2010) ACS Med Chem Lett 1: 331

    Organizational Affiliation

    Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-domain protein kinase 1
A
484Toxoplasma gondiiMutation(s): 0 
Gene Names: CDPK1TgCDPK1
EC: 2.7.11.17
Find proteins for Q9BJF5 (Toxoplasma gondii)
Go to UniProtKB:  Q9BJF5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BK1
Query on BK1

Download CCD File 
A
1-(1-methylethyl)-3-(naphthalen-1-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C19 H19 N5
QFGDRGRJMYSRIW-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BK1IC50:  66   nM  PDBBind
BK1IC50:  130   nM  BindingDB
BK1IC50:  66   nM  Binding MOAD
BK1IC50:  128   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.243α = 90
b = 72.851β = 98.78
c = 65.713γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description